OSTON — Everyone was so sure the newborn would die that they didn’t even clean him off after birth. Nurses didn’t weigh him, or suction fluid out of his throat.

His parents had bought no baby supplies, other than a single onesie. They expected to bury him in it.

But Bentley Yoder came out screaming and wouldn’t give up.

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A significant chunk of his brain grew outside his skull, in a bulbous mass at the top of his head. With birth defects like his, the protruding white matter is usually such a mess that doctors just lop it off. But Bentley had so much brain outside his skull that doctors thought it must be crucial to his survival.

That presented an enormous medical challenge, his parents and doctors explained to STAT last week. The lead surgeon had never seen a case quite like this — and there were no textbooks to guide any of them through it.

Do nothing and Bentley almost certainly wouldn’t make it. Like a balloon filled with too much air, his skin was stretching thin over the mass as his brain grew and filled with fluid. If the bulb burst, he would surely die of an infection.

Operating was also a tremendous risk. The brain material was too big to fit back in his skull. And Bentley’s situation was so unusual, doctors couldn’t predict what would happen once they shaved off his luxurious light brown curls and cut into the mass.

Their quest to give Bentley a future would lead his parents, Dustin and Sierra Yoder, from their small town in Ohio to Boston Children’s Hospital, which just completed a $12 million surgical simulation center to help doctors practice difficult operations before making the first incision.

Even with that practice, however, the surgery was daring. The Yoders, both 25, went ahead with it anyway, late last month. They felt they had to choose the only alternative that offered hope.

The Yoder family in Boston, before Bentley’s surgery.Katherine C. Cohen/Boston Children’s Hospital

Diagnosis: ‘incompatible with life’

Dustin and Sierra Yoder have always known each other. They grew up together in Sugar Creek, Ohio, population 2,200. They have a photo of them both at age 2. They’re kissing.

In high school, Dustin was too wild for Sierra’s taste; he teased her whenever they met. Her mother said it was because he liked her. Sierra decided he was just mean. “You didn’t make my life easy through school, either,” Dustin said quietly. “You didn’t give me the time of day.”

They married in 2012, when they were both 21. Sierra worked in a pizza shop; Dustin installed garage doors. Their first son, Beau, was healthy.

But at the 22-week mark of her second pregnancy, her boss noticed something amiss in Sierra’s ultrasound.

Two days later, after a higher-resolution scan, Sierra and Dustin were told that their unborn child had a rare and often fatal birth defect called an encephalocele, in which the skull doesn’t form properly. Like other neural tube defects, it may have been caused by a vitamin deficiency, although Sierra had religiously taken her prenatal vitamins.

The defect meant that Bentley had a hole at the top of his skull. So his brain was growing along the path of least resistance: up and out.

The doctor “just kept saying that the baby would be ‘incompatible with life,’” Sierra recalled.

Because Sierra was already more thanmid-way through the pregnancy, specialists told the couple they essentially had one day to decide whether to get an abortion. At first, the prognosis was so overwhelming and hopeless, they said yes.

That night, Dustin turned on his favorite techno music to try to relax. Sierra felt the fetus kicking and turning inside of her, as if responding to the beat. He felt so alive. How could he be incompatible with life?

A ‘mama bear’ fights back

Sierra went into labor on Halloween, wearing a shirt she’d decorated with a pumpkin drawn over her big belly. Although she and Dustin had been told their son wouldn’t live more than a few hours, they were excited to finally meet him. They hoped to hold him before he passed.

After nine hours of labor, early on Nov. 1, Sierra delivered her son. She was able to hold him.

Thirty-six hours later, she and Dustin were still holding him, still waiting for the worst.

Bentley did struggle: Twice during his first month, doctors told the Yoders there was nothing they could do other than keep him comfortable as he died. He was hospitalized twice before his half-birthday, as his tiny body struggled to fight off infections.

Again and again, Sierra and Dustin braced themselves and 3-year-old Beau for Bentley’s death.

The Yoders went to three local hospitals but couldn’t find a doctor with expertise in this type of case. By this point an Internet expert on encephaloceles, Sierra tracked down Dr. John Meara at Boston Children’s Hospital. He has performed more such surgeries than anyone else in North America.

He agreed there was a chance to save Bentley’s life.

Meara developed a plan to slice Bentley’s skull in several places and spread it out like a flower to make more room. To close the encephalocele, he planned to take two segments of skull from elsewhere and criss-cross them at the top of the baby’s head.

To test his idea, the surgeon sent Bentley’s brain scans to a 3-D printer at Boston Children’s and turned the resulting plastic model over and over in his hands. He sliced it up, and sent it back to the lab to get a sense of how much more material he could fit inside Bentley’s skull.

In consultation with neurosurgeon Dr. Mark Proctor, Meara decided it might be just enough to fit all of Bentley’s brain.

But when to do the surgery? He needed to let the baby grow a bit until his skull was sturdy enough to support the surgery. But he couldn’t wait too long or the encephalocele might rupture.

He settled on May. Bentley would be nearly 7 months old.

Dr. John Meara of Boston Children’s hospital holds a 3-D model of Bentley’s skull and brain, showing the encephalocele.Jeffery DelViscio/STAT

A high-tech rehearsal

Boston Children’s recently completed a $12 million upgrade to its surgical simulation capabilities. The new center is part high school wood shop, part Hollywood special effects lab; it includes two $300,000 3-D printers and a full-scale operating room.

Like Children’s, many hospitals today are experimenting with high-tech approaches to rehearse surgery, much the way flight simulators help pilots practice flying.

Experts in special effects design “dummies” with realistic beating hearts and other features used in doctor training. And companies, such as Surgical Theater of Ohio, allow surgeons (and patients) to visually cruise through a precise replica of the patient’s body or brain.

Eventually, doctors hope to use 3-D printers to manufacture spare body parts, printing out live cells, instead of plastic.

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Proctor said they could have operated on Bentley without a 3-D printout of the boy’s skull, but holding the model in their hands gave the surgeons a much better idea of what they would have to deal with in the operating room. Without that kind of prep, the surgery might have taken 14 hours, the doctors said. Now, they hoped to complete it in four or five.

“It let us know what part of the brain we could replace back into the skull and what part we couldn’t,” Proctor said. “I think we understood things pretty well going in.”

Even so, it was risky. Even Meara was nervous. The night before the surgery, he admits, he slept “not as well as usual.”

Captain Awesome defies the odds

Once again, Bentley defied the odds. The May 24 surgery went well, though he needed two follow-up procedures to add a shunt, draining excess fluid from his brain. (All of the procedures were funded by Ohio state Medicaid.)

Wearing a onesie printed with “Captain Awesome,” Bentley nestled calmly in his mother’s arm the other day at Children’s Hospital.

He squirmed from time to time, aimed his crystal blue eyes at the ceiling, sucked on — and lost — his pacifier, and occasionally made grunting noises.

“Yeah, tell them about it,” Sierra cooed to Bentley when his vocalizations interrupted the tale of his extraordinary life.

The Yoder family after the successful operation.Jeffery DelViscio/STAT

More smiles from Bentley

As crazy as the last year has been, Dustin — who now works as a hospital maintenance supervisor — said the couple is stronger than before.

Sierra finished his thought: “We’ve always been a strong couple, but we’ve never had to fight as hard as we had to fight for Bentley.”

No one knows how much of Bentley’s brain is functional, how “normal” he may eventually become. Most babies with encephalocele have developmental delays.

At least part of the brain that was outside his head controlled vision. Though there are some indications that Bentley can see, it’s not clear how much. Doctors would normally do a brain scan to identify a baby’s vision deficits. But his brain is too unusual to provide guidance, Proctor said.

The Yoders made the long drive back to Ohio last week. Bentley is adjusting back to the daily rhythms of home, and learning to move his head now that it’s been drained of excess fluid and is nearly a pound lighter. He’s starting to interact and smile more.

He’ll begin physical therapy later this month, to give him the best shot at a full life.

“Nobody has any idea of what this kid is actually going to be able to do, because he’s so different,” Sierra said. “Even the fact that he’s meeting some of his milestones is a blessing, so we’re just taking it one day at a time.”

Throughout the emotional roller-coaster of the last year, Dustin said he has found an inner peace: “I’m not really afraid of anything anymore.”

If children like this are saved will they be more likely to give birth to children with similar defects? Evolution leads to a stronger species by eliminating the weaker and defective genes. I’m not saying he shouldn’t be saved. I’m asking if we are ready for the end result?